Yes. They're considering everything from pictographs up to the level of hostile architecture. The proposed message includes instructions to update the message in the language spoken at the time, in the hope of helping the message endure for generations more.
Unfortunately, I don't think any of these ideas will work quite as well as people think they do. Okay, they kind of figured that one out in the full study (they give between a 10-40% probability that a low technology society will understand the warnings) but still. Just looking at human history, mythology and media will tell you how well deterring people from a location through warnings and scary geography has worked out.
The spikes, skeletons and other deterrances are the kind of thing any future historian (or Indiana Jones style explorer) is going to find extremely interesting regardless of warnings. Even if they do know about nuclear radiation.
A future archeologist exploring the architecture is of no concern. A future environmental science team drilling down to study how well our containment procedures worked is of no concern. If people are aware of what's buried, it's not a problem.
The goal isn't to keep people out, per se, it's to let them know what's there. That's what the document proposes. None of the architecture is designed to physically prevent people from entering the site. It's all designed to tell people what's there.